[Molvis-list] polygons

[Sinasi Ellialtioglu]

Dear Miguel, Abhijit, and Inbal,

I thank you all for your comments and guidiance.
With all I know about Rasmol I can obtain octahedra but I don't know a 
way to make its
surfaces as solid or semi-transparent. I enclose a simple case of a 
perovskite pdb file, and
a script file to be implemented afterwards:

abo3.pdb

ATOM      1  o   Ti  d   2       8.000   8.000   8.000      1  24.00
ATOM      2  s   O   b   3       8.000   8.000   4.000      1  60.00
ATOM      3  s   O   b   3       8.000   4.000   8.000      1  48.00
ATOM      4  s   O   b   3       4.000   8.000   8.000      1  36.00
ATOM      5  s   O   c   3      12.000   8.000   8.000      1  36.00
ATOM      6  s   O   c   3       8.000  12.000   8.000      1  48.00
ATOM      7  s   O   c   3       8.000   8.000  12.000      1  60.00
ATOM      8  d   Sr  a   1       4.000   4.000   4.000      1  12.00
ATOM      9  d   Sr  a   1      12.000   4.000   4.000      1  12.00
ATOM     10  d   Sr  a   1       4.000  12.000   4.000      1  12.00
ATOM     11  d   Sr  a   1      12.000  12.000   4.000      1  12.00
ATOM     12  d   Sr  a   1       4.000   4.000  12.000      1  12.00
ATOM     13  d   Sr  a   1      12.000   4.000  12.000      1  12.00
ATOM     14  d   Sr  a   1       4.000  12.000  12.000      1  12.00
ATOM     15  d   Sr  g   1      12.000  12.000  12.000      1  12.00
TER
#CONECT    1    2    3    4    5    0    0
#CONECT    6    1    0    0    0    0    0
#CONECT    7    1    0    0    0    0    0
#
CONECT    2    3    4    5    6    0    0
CONECT    7    3    4    5    6    0    0
CONECT    6    4    5    0    0    0    0
CONECT    3    4    5    0    0    0    0

and abo3.spt

set ambient 60
background white
set boundbox on
color boundbox black
spacefill 0.45
wireframe 0.15
color atoms cpk
rotate y 15
rotate x -15
select 3
spacefill 0.10
wireframe 0.01

If I had only a way to shade a closed surface bounded by CONECT'ed lines....
Anyway, I will visit JMOL solution since it is already there.

Thank you all again.
Sinasi

Miguel wrote:

>>Hi everybody,
>>
>>I am a Rasmol user, and since this list is now bringing together a
>>multi-software society
>>I would like to ask if drawing polygons around oxygen octahedra or
>>tetrahedra in various
>>crystal structures (like in YBCO) is possible in any of Rasmol, Jmol,
>>Chime, Protein Explorer, or else.
>>    
>>
>
>I have recently added rendering of polyhedrons (tetrahedrons and
>octahedrons) to Jmol. They can be rendered as solid or translucent.
>
>The code has not yet been officially released, but is currently in
>prerelease test phase.
>
>There is not much documentation either, but there are only a few commands
>and it is pretty straightforward.
>
>Check out www.jmol.org
>
>Download the prerelease version from sourceforge at:
>
>http://sourceforge.net/project/showfiles.php?group_id=23629
>
>Then you can post specific questions on the jmol-users list. Sign up at
>www.jmol.org/lists
>
>
>Miguel
>
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